nuc_cp {Rtapas}

Nuclear and chloroplast dataset of orchids

Description

Data set of nuclear and chloroplast loci of 52 orchid taxa from Kew DNA and Tissue Collection, https://dnabank.science.kew.org/homepage.html (Perez-Escobar et al. 2021).

Usage

data(nuc_cp)

Format

This data set consists of seven objects:

np_matrix

Associations one-to-one between the 52 orchid taxa. A binary matrix with 52 rows (nuclear) and 52 columns (chloroplast).

NUCtr

Phylogeny constructed by sequence data of nuclear loci of orchids (Perez-Escobar et al. 2021). An object of class "phylo" containing the details of the phylogenetic tree (i.e. edge, edge length, nodes and tips names).

CPtr

Phylogeny constructed by sequence data of chloroplast loci of orchids (Perez-Escobar et al. 2021). An object of class "phylo" containing the details of the phylogenetic tree (i.e. edge, edge length, nodes and tips names).

NUC_500tr

500 bootstrap replicates trees from Perez-Escobar et al. (2021). Object of class "multiphylo" containing a 500 phylogenetic trees with their respective details (i.e. edges, edges length, nodes, and tips names).

CP_500tr

500 bootstrap replicates trees from Perez-Escobar et al. (2021). Object of class "multiphylo" containing a 500 phylogenetic trees with their respective details (i.e. edges, edges length, nodes, and tips names).

pp_treesPACo_cong

Matrix with the value of the PACo statistics generated for each pair (H and S) of posterior probability trees maximizing congruence between them.

pp_treesPACo_incong

Matrix with the value of the PACo statistics generated for each pair (H and S) of posterior probability trees maximizing incongruence between them.

Source

Perez-Escobar O.A., Dodsworth S., Bogarin D., Bellot S., Balbuena J.A., Schley R., Kikuchi I., Morris S.K., Epitawalage N., Cowan R., Maurin O., Zuntini A., Arias T., Serna A., Gravendeel B., Torres M.F., Nargar K., Chomicki G., Chase M.W., Leitch I.J., Forest F., Baker W.J. (2021). Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. American Journal of Botany, 108(7), 1166-1180.

References

Perez-Escobar O.A., Dodsworth S., Bogarin D., Bellot S., Balbuena J.A., Schley R., Kikuchi I., Morris S.K., Epitawalage N., Cowan R., Maurin O., Zuntini A., Arias T., Serna A., Gravendeel B., Torres M.F., Nargar K., Chomicki G., Chase M.W., Leitch I.J., Forest F., Baker W.J. (2021). Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. American Journal of Botany, 108(7), 1166-1180.